Secondary structure and small RNA-seq evidence for dme-mir-2495

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chr2L:5068555-5068699 + CGTATGTAT---------------------TATACATGTATGATCACATTGGCTTGTGGGCGTGG--CAC-TTCAATTGGGCTGACTTTGCCTGGCTGGAAAAGCGGCA-CCTAATTGAAATGC-CCGC---CGATCAGT-GCTCGATTACGAT------CGACACAAGCGACATT---TTCGT-----------------
droSim1 zds89d09.b1:77-211 + CATACGTACAT----------------------ACATGTATGATC-CATTGGCTTGTGGGCGCGG--CAC-TTCAATTGGGCTGACTTTGCCTGGCTGGAAAAGCGGCA-CCTAATTGAAATGC-CCGC---CAATC---------------------------------GACATT---TTCGTTTAATTTCGTTTCTAGC
droSec1 super_5:3155468-3155580 + CGTACAT--------------------------ACATGTATGATC-CATTGGCTTGTGGGCGTGG--CAC-TTCGATTGGGCTGACTTTGCCTGGCTGGAAAAGCGGCA-CCTAATTGAAATGC-CCGC---CAATC---------------------------------GACATT---TTCGT-----------------
droYak2 chr2L:10456243-10456376 - TATAC---------------------------------TATAAT--CATTGGCTTGTGGGCGTGG--CAC-TTCAATTGGTCTGACTTTGCCCGACTGGAAAAGCGGCA-CCTAATTGAAATGC-CCGCCA-CAATCAGT-GCTCGATCGTGAT------CGACACAAGCGACATT---TTCGT-----------------
droEre2 scaffold_4929:5148425-5148554 + TTTATG------------------------------------ATC-CATTGGCTTGTGGGCGTGG--CAC-TTCAATTGGTCTGACTTTGCCCGGCTGGAAAAGCGGCA-CCTAATTGAAATGC-CCGC---CAAACAGT-GCTCGACCATGAT------CGGCACAAGCGACATT---TTCGT-----------------
droAna3 scaffold_12916:13706207-13706309 + CATATG-----------------------------------------------TTGTGGGCGTGG--CAC-TTCAATTGGTCTAACTTTCCCGGAATGGTAAAGCAGTCACTTAATTGAAATGC-CCGC---CAATC---------------------------ACGAGCAACATTTTTTTCGT-----------------
dp4 chr4_group4:1588263-1588389 + TGTCTGTGTGCG----------------------------------CATTGGGTTG-GGGCGTGG--CAC-TTCAATTTGGC--GCTTTGCCTGGCTGTAAAAGCTGCA-ACTAATTGAAATGT-CCGC---CAATCAATTAAGCAA---TAAA------CAACATAAGCAACACT---TTCGA-----------------
droPer1 super_10:591769-591895 + TGTCTGTGTGCG----------------------------------CATTGGGTTG-GGGCGTGG--CAC-TTCAATTTGGC--GCTTTGCCTGGCTGTAAAAGCTGCA-ACTAATTGAAATGT-CCGC---CAATCAATTAAGCAA---TAAA------CAACATAAGCAACAAT---TTCAA-----------------
droWil1 scaffold_180703:1359544-1359639 + TTCACAC----------------------------------------ATTCGTTTTTGTCTATGG--TATTTTCAATTTGGCTC-CTTTATCTGGCTGAAAAAGCTGCA-ACTAATTGAAATGC-CCAT---TTAAC-------------------------------------TT---TATAT-----------------
droVir3 scaffold_12963:10059299-10059444 - CGTATGTGTGTGTGTGTGTGTGTCTGTGTCTGTGTTTGTGTGTGTGCTTTTGATTGAGAACGTTT--CAT-TTCAATTTGGC--GCTTTGCCTGGCTGGAAAAGCTGCA-TTTAATTGAAATGC-GCGTCGCTAAT-AA---TTC-------------------------AATAATT--TATTA-----------------
droMoj3 scaffold_6500:1220428-1220559 + TTTGAGT----------------------------------------ATCA-TTTTAGGGCGTGTTCCAT-TTCAATTTGGC--GCTTTGCCTGGCTGGAAAAGCTGCA-TTTAATTGAGATGC-GCGT---CGACATTTTATTCGATTACATTTAGTTTAATTACAAGAAATATT---TAAGC-----------------
droGri2 scaffold_15252:11801593-11801729 + TGTGTGTGTGTG--------CTTCTCTCTCTATCTCTGTATCTCTCTCTCTGGTTGAGGGCGTTC--CAT-TTCAATTTGGCGCTTTTTGTCTGGCTGGAAAAGCTGCACATTAATTGAAATGTCGCGTCGTTAATCAACT--------------------------------AAT---TT-TG-----------------

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chr2L:5068555-5068699 + CGTATGTATTATACATGTATGATCACATTGGCTTGTGGGCGTGGCACTTCAATTGGGCTGACTTTGCCTGGCTGGAAAAGCGG-CACCTAATTGAAATGCCCGCCG--ATCAGTGCTCGATTACGATCGACACAAGCGACATT---TTCGT-----------------
droSim1 zds89d09.b1:77-211 + CATACGTAC-ATACATGTATGATC-CATTGGCTTGTGGGCGCGGCACTTCAATTGGGCTGACTTTGCCTGGCTGGAAAAGCGG-CACCTAATTGAAATGCCCGCCA--ATC--------------------------GACATT---TTCGTTTAATTTCGTTTCTAGC
droSec1 super_5:3155468-3155580 + CGTAC-----ATACATGTATGATC-CATTGGCTTGTGGGCGTGGCACTTCGATTGGGCTGACTTTGCCTGGCTGGAAAAGCGG-CACCTAATTGAAATGCCCGCCA--ATC--------------------------GACATT---TTCGT-----------------
droYak2 chr2L:10456243-10456376 - TATAC------------TATAAT--CATTGGCTTGTGGGCGTGGCACTTCAATTGGTCTGACTTTGCCCGACTGGAAAAGCGG-CACCTAATTGAAATGCCCGCCACAATCAGTGCTCGATCGTGATCGACACAAGCGACATT---TTCGT-----------------
droEre2 scaffold_4929:5148425-5148554 + TTT---------------ATGATC-CATTGGCTTGTGGGCGTGGCACTTCAATTGGTCTGACTTTGCCCGGCTGGAAAAGCGG-CACCTAATTGAAATGCCCGCCA--AACAGTGCTCGACCATGATCGGCACAAGCGACATT---TTCGT-----------------
droAna3 scaffold_12916:13706207-13706309 + CATATG--------------------------TTGTGGGCGTGGCACTTCAATTGGTCTAACTTTCCCGGAATGGTAAAGCAGTCACTTAATTGAAATGCCCGCCA--ATC--------------------ACGAGCAACATTTTTTTCGT-----------------
dp4 chr4_group4:1588263-1588389 + TGTCTGT-----------GTG--CGCATTGGGTTG-GGGCGTGGCACTTCAATTTGGC--GCTTTGCCTGGCTGTAAAAGCTG-CAACTAATTGAAATGTCCGCCA--ATCAAT--TAAGCAATAAACAACATAAGCAACACT---TTCGA-----------------
droPer1 super_10:591769-591895 + TGTCTGT-----------GTG--CGCATTGGGTTG-GGGCGTGGCACTTCAATTTGGC--GCTTTGCCTGGCTGTAAAAGCTG-CAACTAATTGAAATGTCCGCCA--ATCAAT--TAAGCAATAAACAACATAAGCAACAAT---TTCAA-----------------

Small RNA-sequencing read pileup

Species Read pileup
droSim1
CATACGTAC-ATACATGTATGATC-CATTGGCTTGTGGGCGCGGCACTTCAATTGGGCTGACTTTGCCTGGCTGGAAAAGCGGCACCTAATTGAAATGCCCGCCAATC---------------------------GACATTTTCGTTTAATTTCGTTTCTAGCSizeHit CountTotal NormTotalGSM343915
Embryo
No Reads
dp4
TGTCTGTGT-----------G--CGCATTGGGTTG-GGGCGTGGCACTTCAATTTGGC--GCTTTGCCTGGCTGTAAAAGCTGCAACTAATTGAAATGTCCGCCAATCAATTAAGCA---ATAAACAACATAAGCAACACTTTCGA-----------------SizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
No Reads

Secondary Structure

dm3

dG=-35.2,  p-value=0.009901 dG=-35.2,  p-value=0.009901 dG=-34.4,  p-value=0.009901 dG=-34.4,  p-value=0.009901 dG=-34.3,  p-value=0.009901

droSim1

dG=-35.4,  p-value=0.009901 dG=-35.4,  p-value=0.009901 dG=-34.6,  p-value=0.009901 dG=-34.6,  p-value=0.009901 dG=-34.5,  p-value=0.009901

droSec1

dG=-35.1,  p-value=0.009901 dG=-35.1,  p-value=0.009901 dG=-34.3,  p-value=0.009901 dG=-34.3,  p-value=0.009901 dG=-34.2,  p-value=0.009901

droYak2

dG=-32.1,  p-value=0.009901 dG=-32.0,  p-value=0.009901 dG=-32.0,  p-value=0.009901

droEre2

dG=-32.1,  p-value=0.009901 dG=-32.0,  p-value=0.009901 dG=-32.0,  p-value=0.009901

droAna3

dG=-25.0,  p-value=0.009901 dG=-25.0,  p-value=0.009901 dG=-24.7,  p-value=0.009901 dG=-24.7,  p-value=0.009901 dG=-24.5,  p-value=0.009901

dp4

dG=-24.6,  p-value=0.009901 dG=-24.6,  p-value=0.009901 dG=-24.6,  p-value=0.009901 dG=-24.6,  p-value=0.009901 dG=-24.4,  p-value=0.009901

droPer1

dG=-24.6,  p-value=0.009901 dG=-24.6,  p-value=0.009901 dG=-24.6,  p-value=0.009901 dG=-24.6,  p-value=0.009901 dG=-24.4,  p-value=0.009901

droWil1

dG=-15.7,  p-value=0.009901 dG=-15.7,  p-value=0.009901 dG=-15.7,  p-value=0.009901 dG=-15.7,  p-value=0.009901 dG=-15.3,  p-value=0.009901

droVir3

dG=-22.3,  p-value=0.009901 dG=-22.3,  p-value=0.009901 dG=-21.7,  p-value=0.009901 dG=-21.7,  p-value=0.009901 dG=-21.3,  p-value=0.009901

droMoj3

dG=-26.3,  p-value=0.009901 dG=-26.3,  p-value=0.009901 dG=-25.7,  p-value=0.009901 dG=-25.7,  p-value=0.009901 dG=-25.3,  p-value=0.009901

droGri2

dG=-24.8,  p-value=0.009901 dG=-24.0,  p-value=0.009901 dG=-23.8,  p-value=0.009901

Generated: 03/07/2013 at 04:57 PM